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Flashcards in Test 2 Deck (100)
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0
Q

DNS

A

Chain of nucleotides aka polynucleotide
Double helix
5’ to 3’

1
Q

Gene

A

Functional unit of genetic information
Located on chromosomes or other genetic elements in cell
Composed of DNS

2
Q

DNa bases (pyrimidine)

A

Cytosine: DNa and rna

Thymine: Dna only

3
Q

Purine bases(dna)

A

Adenine and guanine: both dna and rna

4
Q

Watson and crick

A

Proved DNa had double helix structure with sugar and I hospital groups with nitrogen bases.

5
Q

Wilkins and Rosalind Franklin

A

Were a huge part of Dna helix discoveration, Franklin used x rays diffraction images

6
Q

the double helix

A
All cells
Bacteria:millions of nucleotides 
Two strands are anti palRallel
A-t , g - c
High heat breaks hydrogen bonds, gc rich melts at higher temp them at
7
Q

Size=length

A
Measured in base pairs
1000 base pairs = 1kbp
1000000 base pair is mega base pair
E. coli has 4.64 Mbps
.34nm along helix, ecoli is 1 mm
8
Q

Genetic information flow

A

Central dogma of molecular bio: dna>rna>protein

9
Q

Replication

A

Dna is duplicated

10
Q

Transcription

A

Information from dna is transferred to mRNA…NOTE bottom strand

11
Q

Translation

A

Information in rna builds proteins

12
Q

Supercooled dna

A

Further twisted to save space
Negative :unwound
Positive:overwound

Relaxed dna..number of turns predicted by number of base pairs

13
Q

Dna gyrate

A

One part of circle is laid over other
Helix makes contact in two places
Unbroken helix is passed through the break
Following dna gyrate activity two super coils result

14
Q

Genome

A

Entire complement of genes in cell or virus

15
Q

Chromosome

A

Main genetic element in prokaryotes

encoding Core functions

16
Q

Horizontal gene transfer equation

A

N=No X 2^n

17
Q

Horizontal transfer

A

Transfer of genetic material from one bacterial cell to another , related or not related
Antibiotic resistance :1950
Today:who,cdc: a health crisis…post antibiotic era

18
Q

Three mechanisms

A

Transformation
Conjugation
Transduction

19
Q

Conjugation

A

Transfer of dna from a donor to recipient after cell contact via plasmid

20
Q

Transduction

A

Transfer of dna between bacteria via bacteriophages

21
Q

Transformation

A

Uptake of naked dna

22
Q

Plasmids

A

Replicons,circular or linear, replicate separately from chromosomes
Mobile genetic mosaics that spread multiple beneficial traits,drug resistance,virulence…important in bacterial evolution and adaptation
Most bacteria have a lot of them
Hi vs low copy number , self transferable, difference in host range

23
Q

Reason for Increase in resistance

A

In gram neg bacteria is due to mobile genes in plasmid

24
Q

Virulence

A
Encoded in plasmids
Enables pathogen to colonize
Enables pathogen to damage host 
Hemolysis
Enterotoxin
25
Q

Transposable elements

A

Segment of dna that can move from one site to another site on same or different dna molecule
Types:insertion sequences,transposing, special viruses

26
Q

Viruses

A

Contain either dna or rna genomes
Linear or circular
Single or double stranded

27
Q

E. coli chromosome

A

Lab strain: 4.64 Mbps
0157: h7 5.5 mbp
40 percent of predicted proteins are unknown function
Average protein: 300 amino acids=900 bp=1kbp

28
Q

Semi conservative (dna replication)

A

Each of two double helices have one parental and one new strand
Replication always goes from 5 triphosphate to 3

29
Q

DNA polymerase

A

Catalyze the additions of dntp
5 different polymerases in ecoli primary is polymeraeIII
DNA POLYMERASES require primer from rna

30
Q

Replication fork

A

DNA synthesis begins at origin of replication in prokaryotes:oriC
Fork is zone of unwound DNA where replication occurs
DNA helices unwinds the DNA

31
Q

Connecting DNA fragments in lagging strand

A
  1. syhnthesis on lagging strand continues until it reaches previous synthesized DNA
  2. DNA polymerase 1 removes rna primer and replaces with DNA
  3. dna ligase seals nick in DNA
32
Q

Bidirectional DNA synthesis in prokaryotes

A

Two replication forks moving in opposite directions

33
Q

Replisome

A

Complex of multiple proteins involved in replication

DNA is pulled through replisome

34
Q

Accuracy of DNA replication

A

Extremely accurate due to proofreading
Errors are extremely rare
Polymerase detect mismatch through incorrect hydrogen bonding

35
Q

Polymerase chain reaction (pcr)

A

1, add DNA template primers, DNA polymerase
Heat and cool
Heat and cool

36
Q

Applications of pcr

A

Surveying different groups of environmental organisms,s
Cloning DNA into plasmids
Identifying specific bacteria
Looking for a specific gene

37
Q

Transcription process

A

Carried out by rna polymerase
Uses DNA as template
Rna precursors are atp,gtp,ctp,utp,
Chain growth is 5 tom3 same as replication
Only one of two strands is transcribed by rna

38
Q

Promoters

A

Site of initiation of transcription

39
Q

Transition terminators

A

Site where transcription stops

40
Q

Operon

A

A group of related genes cotta scribed on a polycistronic(encoding group) mrna

41
Q

Exons and introns

A

Exons are the Coding sequence
Introns are the intervening sequences
Introns rare in archaea

42
Q

Eukaryotic rna processing

A

Many rna molecules are altered before they carry out their role in the cell

43
Q

Rna splicing

A

Takes place in nucleus
Removes introns from rna transcripts
Performed by spliceosome

44
Q

Rna capping

A

Addition of methylated guanine to 5 end mRNA

45
Q

Poly a tail

A

Addition of 100-200 adenlylane residues

stabilizes mRNA and is required for translation

46
Q

Proteins

A

Play major role in cell functions
Catalytic proteins(enzymes)
Structural proteins
Proteins: polymers of amino acids

47
Q

Polypeptide

A

Amino acids linked together y peptide bonds

48
Q

Primary structure

A

Linear array of amino acids in a polypeptide

22 amino acids

49
Q

Genetic code

A

Triplet of nuclei acid bases (codon) encodes a single amino acid
Specific codons for stopping and starting translation

50
Q

Stop codons

A

Uaa uag uga

51
Q

Start codon

A

Aug

52
Q

Open reading frame (orf)

A

Aug followed by codons and a stop codon in same frame

53
Q

Anticodon

A

Three bases on tRNA that recognize codon on mRNA

Wobble irregular base pairing allowed at third position of tRNA

54
Q

Transfer tRNA

A

Atleast one tRNA per amino acid
Bacterial cells have 60 different tRNA
Mammalian cells have 100-110
Specific for both codon and its cognate amino acid
Arp is required to attach amino acid to tRNA

55
Q

Ribosomes

A

Site of protein synthesis
Thousands per cell
Combination of rRNA and protein
E. coli has 52 distinct proteins

56
Q

Translation steps

A

initiatione:two ribosomal subunits assemble with mRNA
Elongation:amino acids are brought to the ribosome and are added to the growing polypeptide , occurs in a and p sites(translocation)
3.termination: occurs when ribosome reaches stop codon,release factors.

57
Q

Polyamory

A

A complex formed by ribosomes simultaneously translating mRNA

58
Q

Antibiotics

A

Inhibit translation by interacting with ribosomes

59
Q

Desaturation

A

When proteins are exposed to extreme heat,ph,or certain Chemicals
Results in loss of biological properties(microwaves)

60
Q

Signal sequences

A

Found on proteins requiring transport from cell
Prevent protein from folding
Found at beginning of protein molecule

61
Q

Genome

A

Complement of genetic information
Includes genes, regulatory sequences , and non coding DNA

Includes chromosome and plasmids

62
Q

Genomics

A

Discipline of mapping, sequencing, and analyzing , and comparing genomes

63
Q

Sequencing

A

Determining precise orders of nucleotides I’m a DNA or rna molecule

64
Q

Illumina sequencing

A

Lucifer are consumes arp and emits light

Light flash detected by sensor

65
Q

Pacific biosciences smrt

A

Single molecule real time sequencing
Reactions carried out in nano containerssingke stranded DNA fragments attached
Complementary strand synthesized our fluorescent tags attached

66
Q

Shot gun sequencing

A

Much of sequencing is redundant

Computer algorithms are used

67
Q

Closed vs draft genome

A

Closed genome relies on manpower
More expensive
More information

68
Q

Bioinformatics

A

Science that applies powerful computational tools to DNA and protein sequences

69
Q

Annotation

A

Converting raw sequence data into a list of genes present in the genome
Majority of genes encode proteins

70
Q

Genomes of organelles

A

Mito and chloroplasts contain a small genome

Also contain the necessary machinery for protein synthesis

71
Q

Chromosomal islands

A

Region of bacterial chromosome of foreign origin that contains clustered genes for some extra property such as:
Virulence
Symbiosis

72
Q

Metagenome

A

The total gene content of the organisms present in environment

73
Q

Major modes of regulation

A
  1. Controls the activity of preexisting enzymes
    Post-translational regulation, very rapid process
    2.other controls amount of enzyme
    Regulates transcription,translations…slower process
74
Q

DNA binding proteins

A

mRNA transcripts have short half life
Regulation requires protein binding to DNA
Small molecules influence binding of regulatory proteins to DNA

75
Q

Outcomes for DNA binding

A
  1. Catalyze a specific reaction. On DNA molecule
  2. The binding event can block transcription
  3. The binding event can activate transcription
76
Q

Control of transcription/translation

A

Resulted by Interactions between small molecules and DNA binding proteins

77
Q

Negative control

A

A regulatory mechanism that stops transcription
Repression
Induction

78
Q

Repression

A

Preventing the synthesis of an enzyme in response to a signal
Affects anabolic enzyme
No wasted energy

79
Q

Induction

A

Production of an enzyme in response to a signal
Affects catabolic enzymes
No wasted energy

80
Q

Inducer

A

Substance that induces enzyme synthesis

81
Q

Corepresser

A

Substance that represses enzyme synthesis

82
Q

Effectors

A

Collective term for inducers and repressors

Affect transcription indirectly by binding to specific DNA binding proteins

83
Q

Operon

A

Cluster of genes arranged in A linear fashion whose expression is under control of single operators
Downstream of promoter
Transcription is physically blocked when repressors bind to operator

84
Q

Iptg

A

Induces beta galactosidase but not hydrolyzed by enzyme

85
Q

Positive control

A

Regular protein activates the binding rna of polymerases to DNA
Maltose catabolism in E. coli
DNA sequence: activator-binding site

86
Q

Activator protein

A

Helps rna polymerase recognize promoter

87
Q

Catabolism repression

A

Example of global control

88
Q

Diauxic growth

A

Two exponential growth phases

89
Q

Catabolite repression

A

Transcription is controlled by an activator protein

Activator protein

90
Q

Cyclic amp

A

Key molecule In many metabolic control systems

91
Q

Quorum sensing:

A

Mechanism by which bacteria assess their population density

Discovered as mechanism regulating light production

92
Q

Regulatory rna molecules

A

Exert their affects by base pairing with mRNA

93
Q

Capsid

A

Protein she’ll that surrounds the genome of a virus particle

94
Q

Capsomere

A

Subunit of the capsid

95
Q

Nucleocapsids

A

Constructed in highly symmetric ways

Helical symmetry…rod shaped viruses

96
Q

Lysozyme

A

Makes hole in cell wall

Lyses bacterial cell

97
Q

Neuraminidases

A

Degrades silicon acid, helps virus assembly

98
Q

Temperate viruses

A

Can undergo a stable relationship within the host but can also kill cells through lyric cycle

99
Q

Lysogeny

A

State where most virus genes are not expressed and virus genome is replicated in synchrony with host chromosome